Ec_RprA,

cmscan-Rfam

Family :

RprA

Id:

RF00034

Type:

Gene; sRNA;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

GO:0003729 mRNA binding

Description:

Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a
double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the
translation initiation site. Clones carrying rprA (RpoS regulator RNA A) increased the translation of RpoS.
The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is
predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate
in the positive regulation of RpoS translation. RprA also appears to bind to the RpoS
leader [2]. RprA is non-essential [1]. The Y. pestis homologue was detected by similarity to
the E. coli gene (pers obs. Bateman A).

Score:

110.6

E-value:

3.3e-18

From sequence:

1

To sequence:

106

Alignments:

                                                                                                                     NC
               :<<<<_____________>>>>,,,,,,,,,<<-<<_____>>->>,,,,,,,,,,,,,,,<<<___>>>,,,,,,,,<<<<<<<______>>>>>>>::: CS
   RF00034   1 AcguuucUAaAuuAAcuuaaugauuuuuAaucaUggaaaUccccugauuGAAauaacGaAUUGCUGUGUGUAGUCUUUGCCcgUCaCCUAaGAcgGGCUUU 101
               ACG:UU+UAAAU+AAC+UA:UGAUUU+UAA CAUGGAAAUCCCCUGA+UGAAA+AACGAAUUGCUGUGUGUAGUCUUUGCCC:UC+CC A GA:GGGCUUU
  Ec_RprA,   1 ACGGUUAUAAAUCAACAUAUUGAUUUAUAAGCAUGGAAAUCCCCUGAGUGAAACAACGAAUUGCUGUGUGUAGUCUUUGCCCAUCUCCCACGAUGGGCUUU 101
               ***************************************************************************************************** PP

                          NC
               :::::~~~~~ CS
   RF00034 102 UUUUU*[2]> 108
               UUUUU     
  Ec_RprA, 102 UUUUU*[0]> 106
               *****..... PP

RNAfold

>Ec_RprA,
cgguuauaaaucaacauauugauuuauaagcauggaaauccccugaguga
aacaacgaauugcuguguguagucuuugcccaucucccacgaugggcuuu
uuuuu
.(.(((((((((((....))))))))))).)..((....)).................(((((.....)))))....(((((((......)))))))........ (-24.80)

Length sequence

: 105

Length match:

105